Rodney's Story
by Page Library Page
Summary: Rodney makes an interesting and protective new friend who helps him stop a sabateur.
1. Chapter 1: It Begins

**Title: **Rodney's Story  
**Fandom: **Stargate Atlantis  
**Blanket Disclaimer:** I write stories for FUN, not money. I don't own any of the characters or places I write with, I just play with them. Again, NOT MINE!  
**Author's note: **Reviews are as addictive as caffeine... GIMME!  
**Summary: **Rodney makes an interesting and protective new friend who helps him stop a sabateur.  
**Warnings:** Un-Betaed. Angsty. Apparently, I like picking on Rodney.

**Chapter One**

* * *

Who is he!?

I thought that my team had begun to trust me again after I destroyed an entire solar system and all of a sudden, HE shows up. All of a sudden, everyone is fascinated with Rod.

Yes, fascinated and leaving me out in the cold. Slowly, but surely, Rod has taken over my job, my life, my friends. I am becoming obsolete in this universe and no one has noticed.

First, it was Jeannie. He became the brother I could never be, asking her opinion at work, pulling her chair out for her at dinner, and laughing with her. My sister forgot how we had played chess for hours against our Grandfather. How we would both team up against him and how he let us win the first time. She had forgotten how hard I tried to keep her safe… she never knew how innocent and ignorant she was to the bruises that covered my body and the blood that stained my clothes.

Then, he enchanted my team. The much praised SGA-1; Shepherd, Teyla, and Ronon, even Dr. Weir and Radek fell to his charm. I was replaced at meals, forgotten when 'team night' came around every week, and ignored by the few people I trusted. The friends I thought I finally had, the friends I thought would always be there for me, weren't.

And lastly, firmly entangled in my life, he screwed me over tenfold by turning Atlantis against me.

"What the HELL were you thinking, Rodney!!!" Shepherd screamed in my face. "You nearly killed us all! If Rod hadn't happened by and seen your mistake, the Wraith would have found us and we would have been dinner!"

"I don't think it was a mistake." Rod said, speaking for the first time since calling the security to Rodney's lab. "The evidence suggests this was done purposely." He stated.

'What!' Rodney thought. What the hell was this imposter saying? Not a mistake? Wait! He's saying ---

"He did this on purpose."

"No, I didn't." Rodney said, forcing the words from his bruised throat. It hurt to talk, it shouldn't have, but since he had been choked while being restrained by the marines only a few minutes ago, it was understandable.

Pulling John over to the corner, as if trying to be discrete, Rod spoke his accusations into my best-friend's ear.

"I didn't want to say anything before, because I'm not from here." He said, waving his hand. "But, Dr. McKay has been making mistakes and threatening me regularly. I don't want to cause any trouble but I feel it's my presence that is making him act this way. If it's alright with you, Colonel Shepherd, I'll go back to earth the next time the Daedelus is here."

"No, Rod, that won't be necessary. I am inclined to believe that you are correct and Dr. McKay is acting out of jealousy. If you don't feel safe around him, I can assign a security detail."

"Oh, thank you. That would make me feel a lot better; I mean the man _is _a genius and could probably kill me without leaving any evidence if I was alone." Rod said, gratefully.

"Wait, John, you can't possibly believe him!" I cried, shocked that I had truly lost my best friend.

"McKay, shut up!!!"

I froze, silent. In all the time I had known John Shepherd, he had never told me to 'shut up', not once. Not when I was babbling about some technology he didn't understand, not when I was whining from a paper cut, and not when I was criticizing his favorite DVD. I think that those words, shouted at me, hurt more than any of the Atlantis' crew's behavior to date.

"Dr. McKay."

I looked up, wondering when I had let my head drop, and saw John's cold eyes glaring at me from across the room.

"You are going to the infirmary so Carson can check you over." He said, rolling his eyes. Any other time, he would have insisted it was some kind of alien technology affecting me, but now he was acting like it didn't matter.

I turned to leave, but stopped at his next words.

"Marine, cuff him and don't let him out of your sight. We don't want anyone else getting hurt." John, no, Colonel Shepherd ordered. If I thought about him as military, it meant I didn't care what he said… it meant that it didn't hurt.

I don't remember walking to the infirmary. I don't remember the stares as I was escorted by two marines who were both nearly twice my size and ten times stronger than I was. I don't remember sitting down on one of the beds and letting Beckett poke and prod to his hearts content.

* * *

**TBC...**


	2. Chapter 2: Meeting Atlantis

**Title: **Rodney's Story  
**Fandom: **Stargate Atlantis  
**Blanket Disclaimer:** I write stories for FUN, not money. I don't own any of the characters or places I write with, I just play with them. Again, NOT MINE!  
**Author's note: **Reviews are as addictive as caffeine... GIMME!  
**Summary: **Rodney makes an interesting and protective new friend who helps him stop a sabateur.  
**Warnings:** Un-Betaed. Angsty. Apparently, I like picking on Rodney.

**Chapter Two**

* * *

*0325 Atlantis Time*

_Rodney. Wake up, Rodney._

"I don't want to wake up. Please, let me stay in this dream," Rodney begged, unashamed of the tears streaming down his face. "I still have them here. My friends are still mine, they still like me."

_Rodney. He is tampering with my security protocols. I need you to stop him; fix this before I am beyond repair._

Rodney shot awake, gasping for breath. His chest still heaving, Rodney looked around the small room he was being held in. He was alone.

_Rodney. Please, you must hurry._

"Who are you? What do you want?" Rodney spoke into the darkness.

_I am the city. I am Atlantis._

"Wait, you're a guy?" Rodney asked.

_I should have expected you to ask the unconventional question first._ Atlantis chuckled_. Yes, I have a male conscience. I can tell you are uncomfortable conversing in this manner…_ "Is this better?"

A bright light flashed in the room and a young man appeared before Rodney. Rodney felt his jaw drop and his eyes go wide. The man was beautiful, like the ancient gods of earth (not the Go'uld); he was almost six feet tall with blonde hair and deep green eyes. Rodney was only a little bit jealous.

Rodney blushed. "Umm, do you have anything else to wear?" he asked, trying to look anywhere but the gorgeous young man in a harem-style outfit.

"Oh, of course," Atlantis replied, sounding slightly embarrassed. "It has been a very long time since I appeared in this form. Living as energy for so long, I have forgotten what you mortals deem appropriate."

Another flash of light, this one softer than the first, and Atlantis was clothed in a pair of tight jeans and a black turtleneck shirt though his feet remained bare.

"Ok, stop, stop, stop! You're ascended?" Rodney asked. "Isn't it against the rules to interfere in mortal affairs?"

"Yes, I am ascended. However, as a mortal, I was bonded to the city. From the time I was conceived, I have been the medium for the city and when I reached ascension, I continued to provide assistance to those inhabiting it." Atlantis closed his eyes, pain flashing across his face.

"Please, he is stripping the security protocols. Your scientists were running a diagnostic and I allowed them into my secured systems. He is going to cause irreversible damage if we do not act now."

"I'd love to help, but I'm kinda stuck in…" Rodney trailed off as the door slid open. "Ok. I like that. What about the marines 'guarding' me?"

"They cannot see you. I have shielded you and as they do not have the gene anyway, they have no chance to see you." Atlantis smirked. "I have no need for them to assist me in guarding prisoners, of which you are not."

"Can they hear me?" Rodney asked. When Atlantis shook is head, he continued. "Can you tell me exactly who and what this person is doing to you?"

"It is the Rodney from the alternate reality. This 'Rod' is attempting to sabotage my defensive programming and disconnect my offensive details."

"Where is he?"

"In your quarters. I believe it is his goal to discredit you further." Atlantis turned to Rodney, who had stopped. Reaching out, Atlantis drew the scientist into his arms. "It will be alright, Rodney. I won't let anyone or anything hurt you."

"Why?" Rodney never could understand why some people hated him and others acted like they liked him. Usually the ones who 'liked' him just wanted him to write their papers for them. And Atlantis' hugging him caused him great confusion. People didn't just go around hugging him, they just didn't.

"Since you arrived, you have taken great pains and gone to great lengths to fix problems, repair damage, and to make it easier for me to interface and run the city. I owe you more than you will ever know, Rodney." Atlantis explained.

"What about Colonel Shepperd? He's got the gene in spades, so why not get his help?"

"Yes, John Shepperd does have the gene and he did wake the city from its slumber, but it was you who reinstated the programming that woke me. I would have continued to sleep, if you hadn't started going through the programming and repairing the interface." Atlantis stepped away, keeping an arm around Rodney's shoulders.

"Now, let's go kick Rod's butt" Atlantis said, grinning madly.

"Ya know, it's a little weird, you remind me of General Jack O'Neill on earth. He was my best friend before I left for the Pegasus galaxy, then Major Shepperd adopted me, well, before he decided to dump me for the 'new and improved Rod'."

"Well, I prefer you. And right now, we need to stop Rod. Later, I would like to hear about this Jack O'Neill of yours."

Rodney nodded his agreement and took off down the hallway, staying right on Atlantis' heels.

* * *

Stepping into his room behind the ascendant, Rodney could see Rod working on his computer. Rod was typing madly and trying to bypass the protocols that were in place to keep him from doing exactly what he was trying to do.

"Rod. You can't win now. I have Rodney with me, if you do not stop what you are doing I will have to cause you damage and then Rodney will fix the mess you've created." Atlantis said, stalking over to the man and leaning down into his shocked face.

"However, if you do stop now, I will let you go without harm. Of course, you will have to confess to everything you have done thus far. But, that would be far less painful than what I have planned for you.

"Rodney, come over here and see if you can fix this mess from this terminal, please." Atlantis beckoned him forward.

Rodney walked to the computer and sat in the quickly evacuated chair. He ignored Rod's retreat and started working. About fifteen minutes later, Atlantis and Rodney both turned to the door. They could hear footsteps advancing quickly towards them.

A screen appeared on the wall in front of Rodney, he wasn't shocked by things like that anymore. He watched the image focus and couldn't help the feeling of despair that came over him. There were twenty marines coming down the hall, accompanied by Dr. Weir, Major Shepperd and the rest of SGA-1, Radek, and of course, Rod.

Stopping in the hall in front of his door, Dr. Weir and Major Shepperd stepped forward.

"Rodney, please come out here." Dr. Weir said. "I think we need to talk."

Rodney turned to Atlantis. "What should I do?" he asked. "They're going to lock me up again and then I won't be able to help you."

"Don't worry Rodney. Let me take care of this. Come along, now." Atlantis straightened from where he was bent over Rodney's shoulder and went to the door. He turned back to Rodney, holding out his hand in an offer of protection. He would protect the scientist with his entire being.

Rodney stood and took the ascendant's hand, allowing Atlantis to pull him through the door to face his co-workers and former friends.

* * *

**TBC...  
Review, please!**


	3. Chapter 3: Life and a Death

**Title: **Rodney's Story  
**Fandom: **Stargate Atlantis  
**Blanket Disclaimer:** I write stories for FUN, not money. I don't own any of the characters or places I write with, I just play with them. Again, NOT MINE!  
**Author's note: **Reviews are as addictive as caffeine... GIMME!  
**Summary: **Rodney makes an interesting and protective new friend who helps him stop a sabateur.  
**Warnings:** Un-Betaed. Angsty. Apparently, I like picking on Rodney.

**Chapter Three**

* * *

**Last time:  
**_"Rodney, please come out here." Dr. Weir said. "I think we need to talk."_

_Rodney turned to Atlantis. "What should I do?" he asked. "They're going to lock me up again and then I won't be able to help you."_

_"Don't worry Rodney. Let me take care of this. Come along, now." Atlantis straightened from where he was bent over Rodney's shoulder and went to the door. He turned back to Rodney, holding out his hand in an offer of protection. He would protect the scientist with his entire being._

_Rodney stood and took the ascendant's hand, allowing Atlantis to pull him through the door to face his co-workers and former friends._

* * *

They found themselves faced with twenty P-90's held in the offensive position.

"You have no authority to be giving orders here." Atlantis said, addressing both Dr. Weir and Colonel Shepperd.

"Who are you?" Dr. Weir said from behind Colonel Shepperd. The major had moved in front of the woman when Rodney stepped through the door with the blonde stranger.

"You could ask Colonel Shepperd, but he won't be able to put the puzzle together because he didn't listen to what I told him." Atlantis admonished the Air Force Colonel.

"Cut the crap. Tell us who you are and what you've done to Rodney!" Major Shepperd ordered.

Rodney stood shocked behind the ascendant. John thought he was being influenced. That disappointed Rodney; he'd thought the Colonel knew him better than that.

"I am this city's keeper and protector. I have chosen Rodney McKay as my own and you will not cause him harm ever again." Atlantis ordered smoothly.

Rodney was shocked. No one had ever willingly chosen him for anything. Ever. To hear such acceptance and desire for him come from an ascended being was almost more than he could comprehend.

"When you came to my city, I slept and would have continued to sleep had Rodney not woken me from my slumber," Atlantis said, stepping forward.

Before Atlantis could continue, Rod shot forward. The man grabbed Rodney by his throat and violently shook him. Rodney's head snapped back and forth from the power of the shaking and he felt himself losing consciousness.

"You!" Rod screamed, "If you wouldn't have interfered, my Masters would have had a new feeding ground! I would have let them feed on all of you, just like I did in my own universe!"

Atlantis' moved faster than the eye could see. In the blink of an eye, he had Rod in the air, dangling from his hand.

"How DARE You!!!" He fumed."Have you heard nothing I've said, you moron. Rodney is MINE! You are nothing more than a bothersome insect compared to him and by the time the rest of these stupid humans figure that out, Rodney will want nothing more to do with them."

Atlantis threw the man down the hall and watched with satisfaction as he came to a stop with a sickening thud. Ignoring the humans standing in silence before him, Atlantis knelt beside Rodney's side.

"I'm sorry Rodney. It has been so long since I interacted with your kind, I have forgotten so much about how you act and react. I promise to watch you more carefully from now on. Please, wake up… I don't know what to do, Rodney, you haven't fixed the medical interface yet. What do I do?" Atlantis pleaded quietly.

The first one to recover from the shock of was Radek Zelenka. Reaching for his earpiece, he called Dr. Beckett on a private line. "Carson? We need you at Rodney's quarters. Yes, he's been injured. Rod? Not sure I care right now. Ok, be quick."

The small Czech stepped forward cautiously. "You are Atlantis are you not?" He asked quietly, ignoring the looks he was getting from the marines and Dr. Weir.

"Yes."

"Why did you appear only to Rodney? Why not Dr. Weir or Major Shepperd?" Radek asked.

"Dr. Weir does NOT have the ancient gene in any form and Major Shepperd is currently acting the fool." Atlantis responded.

Radek stepped forward until he was next to Rodney and Atlantis. He knelt down and took Rodney's pulse. "Well, his heart rate seems a little fast." He commented to himself. "How did we not notice how much weight he has lost? I can't remember seeing him eat anything for nearly 4 days." Radek's eyes opened wide in sudden realization.

"We have to get him to the infirmary now. I think he's gone into shock."

"What do you mean? Shock?"

"He's hypoglycemic. If he doesn't eat enough food, he'll die." Radek said, reaching for the Canadian.

"NO! I will carry him. I do not trust any of you." Atlantis gently picked Rodney up, cradling the too thin form against his chest.

"You, Radek Zelenka, come with me. The rest of you are dismissed to do as you please." He said, before striding swiftly down the hall to the transporter, Radek on his heels.

"Carson, change of plans. We are coming to you in the infirmary; I think Rodney is going into a hypoglycemic coma." Radek said into his COM link. "I am bringing both Rodney and a…" Radek paused, not knowing how to tell the Doctor about Atlantis.

"Radek Zelenka is accompanying Rodney and me to the infirmary, Dr. Carson. I am Atlantis. It was time to show myself to Rodney. Dr. Carson, we need your help." Atlantis said, exiting the transporter and walking into the infirmary.

"Aye, of course." Carson agreed, he had been hearing the melodic voice in his dreams since arriving in the Ancient city. "Put him on this bed, please and stand back. I'll take it from here."

Atlantis did as he was told and retreated a short distance away from the unconscious astrophysicist. Radek followed him and pulled two chairs over for them to sit in.

"Rodney will be fine. He is too stubborn to stay down for long." Radek said. "Tell me, why this has happened?" he asked, referring not only to recent events, but to all of the things that had led up to it.

"It is hard to explain." Atlantis sighed."When your expedition first arrived, I tried reaching out to all of he gene carriers, but none of them responded, so I went back to sleep after completing a threat-assessment. It was months later before I felt the first stirrings of consciousness again… when Rodney began repairing the interfaces that bound me to the city."

Atlantis laughed bitterly."I was not always bound to this city, and as much as I love it, I can't help but wish for freedom once again. My kind, whom you call Ancients, thought it a fine joke sealing my fate to the very city I designed and gave my life to create. I once had a name, a home, lover, and an identity; now, all that was me is bound in this city and I cannot leave."

"Why were you bound to Atlantis?"

"For having the foresight to attempt an alliance with the Wrath. I had discovered the means to remove their need for human nourishment without removing who they were. They could live on as a race, without having the worries of their human 'herds' being culled into extinction. My superiors didn't share my views. They destroyed all of my work and labs before slitting my wrists and allowing my blood to flow into the circuits of the city." Atlantis looked up into the shocked face of Radek Zelenka and tried to explain.

"I already had a link to the city. She and I were connected from my birth and I helped her conscience grow. It was a simple matter to tie our thoughts into one being, even if they chose the crudest form."

John Shepperd stood in complete shock. How could an advanced race like the Ancients do something like that to one of their own? Someone who was trying to fix their mistakes and allow peace back into their galaxy?

* * *

**TBC...  
Reviews, please? *hands out baked goods to all reviewers*  
See, I'm not above bribery.**


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